Team HIV epidemiology and Molecular phylogenetics

The research team on HIV epidemiology is divided into a clinical oriented unit with focus on the undiagnosed population, late testers and HIV continuum of care and an experimental unit with focus on molecular epidemiology, phylogenetics and phylogeography, The two units interact extensively.

The clinical unit has a long-standing experience in describing the high rate of late diagnosis in Sweden, developing methods for quantification of the undiagnosed populations, including the rate of infection among migrants after arrival to Sweden. Together with Public Health England and European Center for Disease Control, a CD4 T-cell trajectory model has been developed to pin-point time of infection. The aim is now to further describe the undiagnosed population and assess whether more advanced methods can be developed for the definition of time of infection.

HIV-1 pol sequences are obtained from 80-90% of newly diagnosed patients in Sweden and evaluated for any presence of predrug treatment resistance (PDR). These sequences are also used for describing the Swedish HIV epidemic with regard to whether persons have been infected before or after arrival to Sweden and to describe transmission clusters. To further enhance the precision of we have developed near-full length genome sequencing using next generation sequencing for most subtypes as well as methodology for studies of minor viral variants. This approach has been found to have a higher precision for describing the phylogenetics with regard to transmission clusters and identification of circulating and unique recombinant forms (CRF, URF).

The sequences are also used for comprehensive investigations of the phylodynamics and phylogeographics of HIV-1 subtypes/CRF/URF circulating in the low-middle income countries of our partners with a large number of clinical samples representing different geographic regions. Moreover, we aim at tracing the date of introduction of HIV-1 in the countries to understand the in depth HIV-1 molecular epidemiology of circulating HIV-1 subtypes and to trace the tMRCA of predominant subtype strains.

Research Team Leader

Johanna Brännström

Research team leader

I am a MD and specialist in Infectious diseases, graduating from Karolinska Institutet in 1998 and defending my thesis on Late Presentation in HIV-1 infection in 2016. I am working as a Senior Consultant at the Clinic of Infectious diseases, Karolinska; mainly at the Centre of HIV Medicine, where I combine clinical work with translational research. I am the representative for Karolinska in the European multicenter study Respond and also the PI for the Swedish “Time” study, which aims at developing and evaluating methodology for assessment of the undiagnosed population as well as for the identification of time of infection.

Research team members

Emmi Andersson

Senior physician MD, PhD

I am MD and consultant in Infectious Diseases and Clinical Microbiology. In my PhD project I am studying HIV-1 infection in Sweden with epidemiological and molecular approaches in a close collaboration between the experimental and clinical units of prof Sönnerborgs research group. I focus on surveillance of transmitted drug resistance with comparative studies of traditional Sanger sequencing and modern NGS technique. Data are analysed with regard to drug resistance mutations in minor viral variants and phylogenetic analysis including identification of transmission cluster. Also we will use the data for the development and evaluation of new and better methods to estimate time-from-infection and the proportion of undiagnosed HIV-infections in Sweden. The latter is done in collaboration with European Center for Disease Control and prof Andrew Philips at University College London.

Gaetano Marrone


I am the Principal Investigator of a registry based project regarding incidence and risk factors of cardiovascular diseases amongst people living with HIV in Sweden. This project is based on the Swedish national InfCare HIV registry, which is connected with other relevant Swedish population registries e.g. the SwedeHeart registry. Within prof Sönnerborgs research group and in associate professor Veronica Svedhems research team, I am also involved in other on-going HIV collaborative projects in Sweden, e.g. i) patients´ treatment satisfaction with health and care, ii) incidence of HPV induced cancer in HIV infected patients in Sweden; iii) assigning probable country of HIV acquisition among adults born abroad based on a CD4 T-cell trajectory model. In the Ethiopian studies, I am involved in two projects: i) Developing & evaluating a predictive model from routinely used immunological, hematological, & clinical parameters to be used as a screening tool for antiretroviral treatent (ART) failure; ii) Molecular evolution of HIV-1 subtype C and its impact in therapeutic response.

Being a biostatistican by training, I focus mainly on the research methodology part (study design, sampling methods, sample size calculation, statistical analysis, scientific writing and manuscript revisions). Since 2009 I am the course leader for the Research Methodology course, Master in Global Health, and since 2012 also lecturer for KI’s Master in Public Health track Epidemiology.

Tina Carlander

Senior physician MD, PhD

I am a Specialist of Infectious Diseases since 2009, subspecialized in HIV and Hepatitis C. I am currently working as a Senior Consultant at the Department of Infectious Diseases, Västmanland County Hospital Västerås. I joined Sönnerborg HIV research group, Department of Medicine, Karolinska Institutet Huddinge in 2012 and registered as PhD-student in 2014. My PhD-project focuses on register-based epidemiology regarding HPV-related cancer-development in women living with HIV.


Database, bioinformatics, CD4+ T-cell trajectory model, high throughput sequencing, NGS, phylogenetics, phylogeographcis, phyloscanner


  • Swedish National InfCare HIV cohort
  • Public Health Sweden
  • Public Health England
  • European Center for Disease Control
  • Jan Albert, MTC, KI
  • Thomas Leitner, Los Alamos
  • Tom Britton, Stockholm University


  • Stockholm County Council
  • Swedish Physicians Against AIDS Foundation
  • Swedish Research Council
  • Karolinska Institutet Research Foundation Grants